Reproducible cache error

As told to me by @mb1069

## Expected Behavior
`cwltool --cachedir cache study_metaspades_wrapper.cwl wrapper_input.yml`
Correctly uses a previous run, or caches a new run, but no crashes.

Tell us what happens instead

## Workflow Code
[cwl.zip](https://github.com/common-workflow-language/cwltool/files/2492568/cwl.zip)

## Full Traceback
Pending
```pytb
Paste the full traceback in case there is an exception
Run the workflow with ``--debug`` flag for more verbose logging
```

## Your Environment
* cwltool version:
Check using ``cwltool --version``